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(-) Description

Title :  CRYSTAL STRUCTURE OF PORCINE PANCREATIC PHOSPHOLIPASE A2 IN COMPLEX WITH 2-METHOXYCYCLOHEXA-2-5-DIENE-1,4-DIONE
 
Authors :  K. V. Dileep, I. Tintu, P. Karthe, P. K. Mandal, M. Haridas, C. Sadasivan
Date :  11 Jun 09  (Deposition) - 30 Jun 09  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Curcumin Binding, Pla2, Pancreatic Enzyme, Disulfide Bond, Lipid Degradation, Lipoprotein, Metal-Binding, Palmitate, Pyrrolidone Carboxylic Acid, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. V. Dileep, I. Tintu, P. K. Mandal, P. Karthe, M. Haridas, C. Sadasiva
Crystal Structure Of Porcine Pancreatic Phospholipase A2 In Complex With 2-Methoxycyclohexa-2-5-Diene-1, 4-Dione
Frontiers In Life Sci. 2012
PubMed: search  |  Reference-DOI: 10.1080/21553769.2012.689262

(-) Compounds

Molecule 1 - PHOSPHOLIPASE A2, MAJOR ISOENZYME
    ChainsA
    EC Number3.1.1.4
    Organism CommonPIG
    Organism ScientificSUS SCROFA
    Organism Taxid9823
    Other DetailsPANCREAS
    SynonymPHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE, GROUP IB PHOSPHOLIPASE A2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MCW1Ligand/Ion2-METHOXYCYCLOHEXA-2,5-DIENE-1,4-DIONE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MCW2Ligand/Ion2-METHOXYCYCLOHEXA-2,5-DIENE-1,4-DIONE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:6 , PHE A:22 , ASN A:23 , HOH A:509 , HOH A:534BINDING SITE FOR RESIDUE MCW A 500
2AC2SOFTWARETYR A:28 , GLY A:30 , GLY A:32 , ASP A:49 , HOH A:518 , HOH A:520BINDING SITE FOR RESIDUE CA A 501
3AC3SOFTWAREGLU A:71 , SER A:72 , GLU A:92BINDING SITE FOR RESIDUE CA A 502

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1A:11 -A:77
2A:27 -A:124
3A:29 -A:45
4A:44 -A:105
5A:51 -A:98
6A:61 -A:91
7A:84 -A:96

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HSW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HSW)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA21B_PIG66-73  1A:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA21B_PIG117-127  1A:95-105
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PA2_HISPS00118 Phospholipase A2 histidine active site.PA21B_PIG66-73  2A:44-51
2PA2_ASPPS00119 Phospholipase A2 aspartic acid active site.PA21B_PIG117-127  2A:95-105

(-) Exons   (0, 0)

(no "Exon" information available for 3HSW)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:124
 aligned with PA21B_PIG | P00592 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:124
                                    32        42        52        62        72        82        92       102       112       122       132       142    
            PA21B_PIG    23 ALWQFRSMIKCAIPGSHPLMDFNNYGCYCGLGGSGTPVDELDRCCETHDNCYRDAKNLDSCKFLVDNPYTESYSYSCSNTEITCNSKNNACEAFICNCDRNAAICFSKAPYNKEHKNLDTKKYC 146
               SCOP domains d3hswa_ A: automated matches                                                                                                 SCOP domains
               CATH domains 3hswA00 A:1-124 Phospholipase A2                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhhh...............hhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...eee....eee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------PA2_HIS -------------------------------------------PA2_ASP    ------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hsw A   1 ALWQFRSMIKCAIPGSHPLMDFNNYGCYCGLGGSGTPVDELDRCCETHDNCYRDAKNLDSCKFLVDNPYTESYSYSCSNTEITCNSKNNACEAFICNCDRNAAICFSKAPYNKEHKNLDTKKYC 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HSW)

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A   (PA21B_PIG | P00592)
molecular function
    GO:0032052    bile acid binding    Interacting selectively and non-covalently with bile acids, any of a group of steroid carboxylic acids occurring in bile.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004623    phospholipase A2 activity    Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    GO:0050482    arachidonic acid secretion    The controlled release of arachidonic acid from a cell or a tissue.
    GO:0032869    cellular response to insulin stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0015758    glucose transport    The directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0032612    interleukin-1 production    The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0032637    interleukin-8 production    The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0019370    leukotriene biosynthetic process    The chemical reactions and pathways resulting in the formation of leukotriene, a pharmacologically active substance derived from a polyunsaturated fatty acid, such as arachidonic acid.
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0002446    neutrophil mediated immunity    Any process involved in the carrying out of an immune response by a neutrophil.
    GO:0045740    positive regulation of DNA replication    Any process that activates or increases the frequency, rate or extent of DNA replication.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0010524    positive regulation of calcium ion transport into cytosol    Any process that increases the rate of the directed movement of calcium ions into the cytosol of a cell. The cytosol is that part of the cytoplasm that does not contain membranous or particulate subcellular components.
    GO:0048146    positive regulation of fibroblast proliferation    Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
    GO:0050778    positive regulation of immune response    Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PA21B_PIG | P005921fx9 1fxf 1hn4 1l8s 1p2p 1pir 1pis 1sfv 1sfw 1y6o 1y6p 2azy 2azz 2b00 2b01 2b03 2b04 2phi 3fvi 3fvj 3l30 3o4m 3p2p 3qlm 4dbk 4g5i 4o1y 4p2p 5p2p

(-) Related Entries Specified in the PDB File

2azy CRYSTAL STRUCTURE OF PORCINE PANCREATIC PHOSPHOLIPASE A2 IN COMPLEX WITH CHOLATE
2b00 CRYSTAL STRUCTURE OF PORCINE PANCREATIC PHOSPHOLIPASE A2 IN COMPLEX WITH GLYCOCHOLATE
2b01 CRYSTAL STRUCTURE OF PORCINE PANCREATIC PHOSPHOLIPASE A2 IN COMPLEX WITH TAUROCHENODEOXYCHOLATE
2b03 CRYSTAL STRUCTURE OF PORCINE PANCREATIC PHOSPHOLIPASE A2 IN COMPLEX WITH TAUROCHENODEOXYCHOLATE
2b04 CRYSTAL STRUCTURE OF PORCINE PANCREATIC PHOSPHOLIPASE A2 IN COMPLEX WITH GLYCOCHENODEOXYCHOLATE